"Error due to lack of JAVA heap memory while running ocimum2000." #83
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help wanted
Extra attention is needed
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It fails at:
```
/** convenience method to extract list of HtmlP in element
*
* @param htmlElement
* @return
*/
public static List<HtmlP> extractSelfAndDescendantIs(HtmlElement
htmlElement) {
return HtmlP.extractPs(HtmlUtil.getQueryHtmlElements(htmlElement,
ALL_P_XPATH));
}
```
called from
```
DefaultArgProcessor: public List<? extends Element>
extractPSectionElements(CTree cTree) {
List<? extends Element> elements = null;
if (cTree != null) {
cTree.ensureScholarlyHtmlElement();
elements =
HtmlP.extractSelfAndDescendantIs(cTree.getHtmlElement());
}
return elements;
}
```
My guess is it is a huge document and we need to extract the count and then
limit the number of extracted elements.
Will look in the morning.
…On Tue, Feb 26, 2019 at 11:14 AM Ambarish Kumar ***@***.***> wrote:
Run command -
ami-search-new -p /media/ambarish123/AMBARISH/Ocimumproject18feb --dictionary /media/ambarish123/AMBARISH/dictionary/monoterpenes.xml /media/ambarish123/AMBARISH/dictionary/diterpene.xml /media/ambarish123/AMBARISH/dictionary/triterpene.xml /media/ambarish123/AMBARISH/dictionary/insecticides.xml /media/ambarish123/AMBARISH/dictionary/invasivespecies.xml /media/ambarish123/AMBARISH/dictionary/Ocimumspecies.xml /media/ambarish123/AMBARISH/dictionary/phytochemicals.xml country gene drugs plantparts
Error snippet
specific and generic values.
Generic values (AMISearchTool)
================================
basename null
cproject /media/ambarish123/AMBARISH/Ocimumproject18feb
ctree
cTreeList 2117 trees [/media/ambarish123/AMBARISH/Ocimumproject18feb/30
dryrun false
excludeBase null
excludeTrees null
file types []
forceMake false
includeBase null
includeTrees null
log4j
logfile null
verbose 0
Specific values (AMISearchTool)
================================
dictionaryList [/media/ambarish123/AMBARISH/dictionary/monoterpenes.xml, /media/ambarish123/AMBARISH/dictionary/diterpene.xml, /media/ambarish123/AMBARISH/dictionary/triterpene.xml, /media/ambarish123/AMBARISH/dictionary/insecticides.xml, /media/ambarish123/AMBARISH/dictionary/invasivespecies.xml, /media/ambarish123/AMBARISH/dictionary/Ocimumspecies.xml, /media/ambarish123/AMBARISH/dictionary/phytochemicals.xml, country, gene, drugs, plantparts]
dictionaryTop null
dictionarySuffix [xml]
ignorePlugins []
Run time error related JAVA heap memory.
................................................................................Exception in thread "main" java.lang.OutOfMemoryError: Java heap space
at sun.nio.cs.UTF_8.newEncoder(UTF_8.java:72)
at java.lang.StringCoding$StringEncoder.<init>(StringCoding.java:282)
at java.lang.StringCoding$StringEncoder.<init>(StringCoding.java:273)
at java.lang.StringCoding.encode(StringCoding.java:338)
at java.lang.String.getBytes(String.java:918)
at nu.xom.Text.build(Unknown Source)
at nu.xom.NonVerifyingHandler.flushText(Unknown Source)
at nu.xom.NonVerifyingHandler.startElement(Unknown Source)
at org.apache.xerces.parsers.AbstractSAXParser.startElement(Unknown Source)
at org.apache.xerces.impl.XMLNamespaceBinder.handleStartElement(Unknown Source)
at org.apache.xerces.impl.XMLNamespaceBinder.startElement(Unknown Source)
at org.apache.xerces.impl.XMLDocumentFragmentScannerImpl.scanStartElement(Unknown Source)
at org.apache.xerces.impl.XMLDocumentFragmentScannerImpl$FragmentContentDispatcher.dispatch(Unknown Source)
at org.apache.xerces.impl.XMLDocumentFragmentScannerImpl.scanDocument(Unknown Source)
at org.apache.xerces.parsers.DTDConfiguration.parse(Unknown Source)
at org.apache.xerces.parsers.DTDConfiguration.parse(Unknown Source)
at org.apache.xerces.parsers.XMLParser.parse(Unknown Source)
at org.apache.xerces.parsers.AbstractSAXParser.parse(Unknown Source)
at nu.xom.Builder.build(Unknown Source)
at nu.xom.Builder.build(Unknown Source)
at nu.xom.Builder.build(Unknown Source)
at org.contentmine.eucl.xml.XMLUtil.parseQuietlyToDocument(XMLUtil.java:1197)
at org.contentmine.cproject.args.DefaultArgProcessor.getScholarlyHtmlElement(DefaultArgProcessor.java:1381)
at org.contentmine.cproject.files.CTree.ensureScholarlyHtmlElement(CTree.java:1239)
at org.contentmine.cproject.args.DefaultArgProcessor.extractPSectionElements(DefaultArgProcessor.java:1365)
at org.contentmine.ami.plugins.AMIArgProcessor.ensureSectionElements(AMIArgProcessor.java:257)
at org.contentmine.ami.plugins.AMIArgProcessor.runRunMethodsOnChosenArgOptions(AMIArgProcessor.java:228)
at org.contentmine.cproject.args.DefaultArgProcessor.runAndOutput(DefaultArgProcessor.java:1296)
at org.contentmine.ami.plugins.word.WordPluginOption.run(WordPluginOption.java:36)
at org.contentmine.ami.plugins.CommandProcessor.runLegacyPluginOptions(CommandProcessor.java:301)
at org.contentmine.ami.tools.AMISearchTool.runLegacyCommandProcessor(AMISearchTool.java:128)
at org.contentmine.ami.tools.AMISearchTool.runSearch(AMISearchTool.java:112)
issues -
I ran the project into the hard drive. There would not have been lack of
memory space but it raises error. Please resolve.
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--
Peter Murray-Rust
Reader Emeritus in Molecular Informatics
Unilever Centre, Dept. Of Chemistry
University of Cambridge
CB2 1EW, UK
+44-1223-763069
|
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I can reproduce the problem: This needs a rewrite of the search options. |
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Run command -
Error snippet
specific and generic values.
Run time error related JAVA heap memory.
issues -
I ran the project into the hard drive. There would not have been lack of memory space but it raises error. Please resolve.
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